I have moved from mail.app to entourage and I want to completely delete all the files (mail messages) from my computer that are associated with Mail.app so I don't have duplicate files on my HD. What is the best way to do this?

Mail fully supports deleting them from within itself, so do that first. If you are worried that it didn't get done properly, check your home folder's Library folder. In there you will find a folder called Mail. In there is where Mail actually stores its messages. If they are gone from there, they are gone!